Development of the Kazakhstan Y-chromosome haplotype reference database: analysis of 27 Y-STR in Kazakh population


To improve available databases of forensic interest, all Y-STR haplotypes from Kazakh population were presented in this study. The reference database accumulated almost 3650 samples from academic and citizen science. Additionally, 27 Y-STR from Yfiler Plus System were first analyzed in 300 males from Kazakh (Qazaq) populations residing in Kazakhstan. The data is available in the YHDR under accession numbers YA004316 and YA004322. A total of 270 unique haplotypes were observed. Discrimination capacity was 90%. Obtained Y-STR haplotypes exhibited a high intra-population diversity. Analysis of pairwise genetic distances showed lowest RST values from Uighur and Mongolian populations.

This is a preview of subscription content, log in to check access.


  1. 1.

    Kayser M (2017) Forensic use of Y-chromosome DNA: a general overview. Hum Genet 136:621–635.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  2. 2.

    Calafell F, Larmuseau MHD (2017) The Y chromosome as the most popular marker in genetic genealogy benefits interdisciplinary research. Hum Genet 136:559–573.

    Article  PubMed  Google Scholar 

  3. 3.

    Thompson JM, Ewing MM, Frank WE, Pogemiller JJ, Nolde CA, Koehler DJ, Shaffer AM, Rabbach DR, Fulmer PM, Sprecher CJ, Storts DR (2013) Developmental validation of the PowerPlex (R) Y23 system: a single multiplex Y-STR analysis system for casework and database samples. Forensic Sci Int Genet 7:240–250.

    CAS  Article  PubMed  Google Scholar 

  4. 4.

    Gopinath S, Zhong C, Nguyen V, Ge J, Lagacé RE, Short ML, Mulero JJ (2016) Developmental validation of the Yfiler (R) Plus PCR Amplification Kit: an enhanced Y-STR multiplex for casework and database applications. Forensic Sci Int Genet 24:164–175.

    CAS  Article  PubMed  Google Scholar 

  5. 5.

    Purps J, Siegert S, Willuweit S, Nagy M, Alves C, Salazar R, Angustia SMT, Santos LH, Anslinger K, Bayer B, Ayub Q, Wei W, Xue Y, Tyler-Smith C, Bafalluy MB, Martínez-Jarreta B, Egyed B, Balitzki B, Tschumi S, Ballard D, Court DS, Barrantes X, Bäßler G, Wiest T, Berger B, Niederstätter H, Parson W, Davis C, Budowle B, Burri H, Borer U, Koller C, Carvalho EF, Domingues PM, Chamoun WT, Coble MD, Hill CR, Corach D, Caputo M, D’Amato ME, Davison S, Decorte R, Larmuseau MHD, Ottoni C, Rickards O, Lu D, Jiang C, Dobosz T, Jonkisz A, Frank WE, Furac I, Gehrig C, Castella V, Grskovic B, Haas C, Wobst J, Hadzic G, Drobnic K, Honda K, Hou Y, Zhou D, Li Y, Hu S, Chen S, Immel UD, Lessig R, Jakovski Z, Ilievska T, Klann AE, García CC, de Knijff P, Kraaijenbrink T, Kondili A, Miniati P, Vouropoulou M, Kovacevic L, Marjanovic D, Lindner I, Mansour I, al-Azem M, Andari AE, Marino M, Furfuro S, Locarno L, Martín P, Luque GM, Alonso A, Miranda LS, Moreira H, Mizuno N, Iwashima Y, Neto RSM, Nogueira TLS, Silva R, Nastainczyk-Wulf M, Edelmann J, Kohl M, Nie S, Wang X, Cheng B, Núñez C, Pancorbo MM, Olofsson JK, Morling N, Onofri V, Tagliabracci A, Pamjav H, Volgyi A, Barany G, Pawlowski R, Maciejewska A, Pelotti S, Pepinski W, Abreu-Glowacka M, Phillips C, Cárdenas J, Rey-Gonzalez D, Salas A, Brisighelli F, Capelli C, Toscanini U, Piccinini A, Piglionica M, Baldassarra SL, Ploski R, Konarzewska M, Jastrzebska E, Robino C, Sajantila A, Palo JU, Guevara E, Salvador J, Ungria MCD, Rodriguez JJR, Schmidt U, Schlauderer N, Saukko P, Schneider PM, Sirker M, Shin KJ, Oh YN, Skitsa I, Ampati A, Smith TG, Calvit LS, Stenzl V, Capal T, Tillmar A, Nilsson H, Turrina S, de Leo D, Verzeletti A, Cortellini V, Wetton JH, Gwynne GM, Jobling MA, Whittle MR, Sumita DR, Wolańska-Nowak P, Yong RYY, Krawczak M, Nothnagel M, Roewer L (2014) A global analysis of Y-chromosomal haplotype diversity for 23 STR loci. Forensic Sci Int-Gen 12:12–23.

    CAS  Article  Google Scholar 

  6. 6.

    Oh YN, Lee HY, Lee EY, Kim EH, Yang WI, Shin KJ (2015) Haplotype and mutation analysis for newly suggested Y-STRs in Korean father-son pairs. Forensic Sci Int-Gen 15:64–68.

    CAS  Article  Google Scholar 

  7. 7.

    Garcia O, Yurrebaso I, Mancisidor ID, Lopeza S, Alonso S, Gusmao L (2016) Data for 27 Y-chromosome STR loci in the Basque Country autochthonous population. Forensic Sci Int Genet 20:E10–EE2.

    CAS  Article  PubMed  Google Scholar 

  8. 8.

    Iacovacci G, D'Atanasio E, Marini O et al (2017) Forensic data and microvariant sequence characterization of 27 Y-STR loci analyzed in four eastern African countries. Forensic Sci Int Genet 27:123–131.

    CAS  Article  PubMed  Google Scholar 

  9. 9.

    Willuweit S, Roewer L (2015) The new Y chromosome haplotype reference database. Forensic Sci Int Genet 15:43–48.

    CAS  Article  PubMed  Google Scholar 

  10. 10.

    Ismagulov O (1970) Population of Kazakhstan from Bronze Epoch to present: (paleoanthropological research). Nauka Alma-Ata

  11. 11.

    Golden PB (1992) An introduction to the history of the Turkic peoples: ethnogenesis and state-formation in medieval and early modern Eurasia and the Middle East. O. Harrassowitz Wiesbaden

  12. 12.

    Johanson L, Csató É (1998) The Turkic languages. Routledge, London

    Google Scholar 

  13. 13.

    Tynyshpaev M (1925) Materials on the history of Kyrgyz-kazakh people. East Department of Kyrgyz State Press Tashkent

  14. 14.

    Tarlykov PV, Zholdybayeva EV, Akilzhanova AR et al (2013) Mitochondrial and Y-chromosomal profile of the Kazakh population from East Kazakhstan. Croat Med J 54:17–24.

    Article  PubMed  PubMed Central  Google Scholar 

  15. 15.

    Zhabagin M, Balanovska E, Sabitov Z et al (2017) The connection of the genetic, cultural and geographic landscapes of Transoxiana. Sci Rep-Uk 7:3085.

    CAS  Article  Google Scholar 

  16. 16.

    Abilev S, Malyarchuk B, Derenko M, Wozniak M, Grzybowski T, Zakharov I (2012) The Y-chromosome C3*star-cluster attributed to Genghis Khan’s descendants is present at high frequency in the Kerey Clan from Kazakhstan. Hum Biol 84:79–89.

    Article  PubMed  Google Scholar 

  17. 17.

    Balanovsky O, Zhabagin M, Agdzhoyan A et al (2015) Deep phylogenetic analysis of haplogroup G1 provides estimates of SNP and STR mutation rates on the human Y-chromosome and reveals migrations of Iranic speakers. Plos One 10:e0122968.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  18. 18.

    Dulik MC, Osipova LP, Schurr TG (2011) Y-chromosome variation in Altaian Kazakhs reveals a common paternal gene pool for Kazakhs and the influence of Mongolian expansions. Plos One 6:e17548.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  19. 19.

    Nothnagel M, Fan GY, Guo F, He Y, Hou Y, Hu S, Huang J, Jiang X, Kim W, Kim K, Li C, Li H, Li L, Li S, Li Z, Liang W, Liu C, Lu D, Luo H, Nie S, Shi M, Sun H, Tang J, Wang L, Wang CC, Wang D, Wen SQ, Wu H, Wu W, Xing J, Yan J, Yan S, Yao H, Ye Y, Yun L, Zeng Z, Zha L, Zhang S, Zheng X, Willuweit S, Roewer L (2017) Revisiting the male genetic landscape of China: a multi-center study of almost 38,000 Y-STR haplotypes. Hum Genet 136:485–497.

    CAS  Article  PubMed  Google Scholar 

  20. 20.

    Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567.

    Article  PubMed  Google Scholar 

  21. 21.

    Perez-Lezaun A, Calafell F, Comas D et al (1999) Sex-specific migration patterns in central Asian populations, revealed by analysis of Y-chromosome short tandem repeats and mtDNA. Am J Hum Genet 65:208–219.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  22. 22.

    Myres NM, Ekins JE, Lin AA, Cavalli-Sforza LL, Woodward SR, Underhill PA (2007) Y-chromosome short tandem repeat DYS458.2 non-consensus alleles occur independently in both binary haplogroups J1-M267 and R1b3-M405. Croat Med J 48:450–459

    CAS  PubMed  PubMed Central  Google Scholar 

  23. 23.

    Balaresque P, Parkin E, Roewer L et al (2009) Genomic complexity of the Y-STR DYS19: inversions, deletions and founder lineages carrying duplications. Int J Legal Med 123:15–23.

    Article  PubMed  Google Scholar 

  24. 24.

    Poetsch M, Bajanowski T, Pfeiffer H (2012) The publication of population genetic data in the International Journal of Legal Medicine: guidelines. Int J Legal Med 126:489–490.

    Article  Google Scholar 

Download references


We gratefully acknowledge all sample donors who participated in this study. We thank Nazarbayev University students (Aigul Abilmazhinova, Rassul Khakimov, Azamat Bashabayev, Kamila Issabayeva, Dariya Kassybayeva, Akylzhan Zhaken) for the laboratory assistance. We would like to thank Maxim Solomadin and Ayken Askapuli for contributions to this work.


This study received primary support from the Ministry of Education and Science of the Republic of Kazakhstan (Grant No. AP05134955).

Author information




Conceived and designed the experiments: MZ, AA; performed the experiments: AS, IT, DE, SL, AE; analyzed the data: MZ, AS; contributed reagents/materials/analysis tools: AR, AA, SL, AE, IT; wrote the paper: MZ; AS, AA participated in the drafting; study initiation: MZ; read and approved the final version of the paper: all coauthors.

Corresponding author

Correspondence to Maxat Zhabagin.

Ethics declarations

Competing interests

The authors declare that they have no competing interests.

Electronic supplementary material

Fig S1

(PDF 4.80 kb)


(XLSX 782 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Zhabagin, M., Sarkytbayeva, A., Tazhigulova, I. et al. Development of the Kazakhstan Y-chromosome haplotype reference database: analysis of 27 Y-STR in Kazakh population. Int J Legal Med 133, 1029–1032 (2019).

Download citation


  • Central Asia
  • Kazakh
  • Y chromosome
  • YHRD
  • Forensic
  • Population genetics
  • STR